# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:52:28 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-{(1R)-2-[(4-cyano-1,1-dioxidotetrahydro-2H-thiopyran-4-yl)amino]-2-oxo-1-[(trimethylsilyl)methyl]ethyl}morpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Si](C)(C)C[C@H](NC(=O)N1CCOCC1)C(=O)NC2(CC[S](=O)(=O)CC2)C#N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CRL  CRL  N-{(1R)-2-[(4-cyano-1,1-dioxidotetrahydro-2H-thiopyran-4-yl)amino]-2-oxo-1-[(trimethylsilyl)methyl]ethyl}morpholine-4-carboxamide  ligand  58  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CRL
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CRL  N1    N   NH1   0  -0.679   0.9414   3.5784  -1.0675
 CRL  C1    C   C     0   0.766   0.1960   2.6383  -1.7287
 CRL  O1    O   O     0  -0.529  -0.9778   2.8605  -2.0026
 CRL  N2    N   NT    0  -0.518   0.8164   1.4683  -2.0526
 CRL  C2    C   CH2   0  -0.325   2.0264   0.9833  -1.4086
 CRL  C3    C   CH2   0  -0.180   2.8073   0.1047  -2.3692
 CRL  O2    O   O2    0  -0.481   2.0199  -0.9484  -2.8726
 CRL  C4    C   CH2   0  -0.191   0.8906  -0.4435  -3.5495
 CRL  C5    C   CH2   0  -0.311   0.0204   0.4037  -2.6415
 CRL  C6    C   CH1   0  -0.193   0.3538   4.8759  -0.8616
 CRL  C7    C   C     0   0.588   0.0222   5.5394  -2.1961
 CRL  O3    O   O     0  -0.465   0.7293   5.4240  -3.1781
 CRL  N3    N   NH1   0  -0.674  -1.0773   6.3306  -2.1731
 CRL  C8    C   CT    0   0.021  -1.5474   7.0639  -3.3280
 CRL  C9    C   CSP   0   0.167  -1.7377   6.1428  -4.4657
 CRL  N4    N   NS    0  -0.246  -1.9320   5.4497  -5.3616
 CRL  C10   C   CH2   0  -0.452  -0.5588   8.1656  -3.7632
 CRL  C11   C   CH2   0  -0.622  -0.3119   9.1885  -2.6667
 CRL  S1    S   S     0   1.224  -1.8207  10.0491  -2.2473
 CRL  O4    O   OS    0  -0.672  -1.6116  10.8560  -1.0477
 CRL  O5    O   OS    0  -0.678  -2.3301  10.7047  -3.4527
 CRL  C12   C   CH2   0  -0.629  -2.8981   8.6749  -1.8636
 CRL  C13   C   CH2   0  -0.485  -2.9305   7.6617  -3.0007
 CRL  C14   C   CH2   0  -0.772   1.3059   5.7737  -0.0714
 CRL  SI1   SI  SI    0   1.075   1.7830   5.1073   1.6493
 CRL  C15   C   CH3   0  -0.989   0.2478   4.3782   2.4600
 CRL  C16   C   CH3   0  -0.992   3.1316   3.7946   1.5317
 CRL  C17   C   CH3   0  -0.971   2.4340   6.5673   2.6463
 CRL  HN1   H   HNH1  0   0.397   1.9431   3.5702  -1.1758
 CRL  H21   H   HCH2  0   0.245   1.7715   0.4201  -0.5028
 CRL  H22   H   HCH2  0   0.248   2.6800   1.7994  -1.1077
 CRL  H31   H   HCH2  0   0.210   3.1932   0.7248  -3.1903
 CRL  H32   H   HCH2  0   0.247   3.6576  -0.3363  -1.8482
 CRL  H41   H   HCH2  0   0.245   0.3176  -1.2970  -3.9138
 CRL  H42   H   HCH2  0   0.208   1.1997   0.1541  -4.4186
 CRL  H51   H   HCH2  0   0.266  -0.7931   0.8281  -3.2247
 CRL  H52   H   HCH2  0   0.234  -0.4236  -0.2208  -1.8564
 CRL  H6    H   HCH1  0   0.274  -0.5677   4.7566  -0.2857
 CRL  HN3   H   HNH1  0   0.419  -1.7280   6.2036  -1.4126
 CRL  H101  H   HCH2  0   0.290  -0.9503   8.6562  -4.6558
 CRL  H102  H   HCH2  0   0.307   0.3955   7.7239  -4.0419
 CRL  H111  H   HCH2  0   0.305   0.0699   8.7359  -1.7507
 CRL  H112  H   HCH2  0   0.338   0.3969   9.9507  -2.9950
 CRL  H121  H   HCH2  0   0.342  -3.8908   9.0982  -1.7011
 CRL  H122  H   HCH2  0   0.309  -2.5578   8.2530  -0.9172
 CRL  H131  H   HCH2  0   0.314  -3.6168   6.8592  -2.7238
 CRL  H132  H   HCH2  0   0.304  -3.3344   8.1256  -3.9003
 CRL  H141  H   HCH2  0   0.262   2.2093   5.9785  -0.6566
 CRL  H142  H   HCH2  0   0.264   0.8216   6.7433   0.0829
 CRL  H151  H   HCH3  0   0.243  -0.0977   3.4971   1.9160
 CRL  H152  H   HCH3  0   0.246   0.4529   4.0707   3.4870
 CRL  H153  H   HCH3  0   0.244  -0.5734   5.0969   2.4873
 CRL  H161  H   HCH3  0   0.239   2.7585   2.8648   1.1007
 CRL  H162  H   HCH3  0   0.244   3.9711   4.1343   0.9215
 CRL  H163  H   HCH3  0   0.246   3.5227   3.5588   2.5234
 CRL  H171  H   HCH3  0   0.242   2.7252   6.2584   3.6519
 CRL  H172  H   HCH3  0   0.242   3.3121   7.0092   2.1711
 CRL  H173  H   HCH3  0   0.242   1.6818   7.3521   2.7454

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CRL  N1   C1    single  1.370  0.020  1.370
 CRL  N1   C6    single  1.439  0.020  1.439
 CRL  N1   HN1   single  0.890  0.020  1.040
 CRL  C1   O1    double  1.226  0.020  1.226
 CRL  C1   N2    single  1.363  0.020  1.363
 CRL  N2   C2    single  1.454  0.020  1.454
 CRL  N2   C5    single  1.454  0.020  1.454
 CRL  C2   C3    single  1.518  0.020  1.518
 CRL  C2   H21   single  0.970  0.020  1.090
 CRL  C2   H22   single  0.970  0.020  1.090
 CRL  C3   O2    single  1.408  0.020  1.408
 CRL  C3   H31   single  0.970  0.020  1.090
 CRL  C3   H32   single  0.970  0.020  1.090
 CRL  O2   C4    single  1.410  0.020  1.410
 CRL  C4   C5    single  1.516  0.020  1.516
 CRL  C4   H41   single  0.970  0.020  1.090
 CRL  C4   H42   single  0.970  0.020  1.090
 CRL  C5   H51   single  0.970  0.020  1.090
 CRL  C5   H52   single  0.970  0.020  1.090
 CRL  C6   C7    single  1.527  0.020  1.527
 CRL  C6   C14   single  1.529  0.020  1.529
 CRL  C6   H6    single  0.970  0.020  1.090
 CRL  C7   O3    double  1.216  0.020  1.216
 CRL  C7   N3    single  1.355  0.020  1.355
 CRL  N3   C8    single  1.447  0.020  1.447
 CRL  N3   HN3   single  0.860  0.020  1.020
 CRL  C8   C9    single  1.476  0.020  1.476
 CRL  C8   C10   single  1.543  0.020  1.543
 CRL  C8   C13   single  1.542  0.020  1.542
 CRL  C9   N4    triple  1.149  0.020  1.149
 CRL  C10  C11   single  1.520  0.020  1.520
 CRL  C10  H101  single  0.970  0.020  1.090
 CRL  C10  H102  single  0.970  0.020  1.090
 CRL  C11  S1    single  1.787  0.020  1.787
 CRL  C11  H111  single  0.970  0.020  1.090
 CRL  C11  H112  single  0.970  0.020  1.090
 CRL  S1   O4    double  1.461  0.020  1.461
 CRL  S1   O5    double  1.464  0.020  1.464
 CRL  S1   C12   single  1.788  0.020  1.788
 CRL  C12  C13   single  1.523  0.020  1.523
 CRL  C12  H121  single  0.970  0.020  1.090
 CRL  C12  H122  single  0.970  0.020  1.090
 CRL  C13  H131  single  0.970  0.020  1.090
 CRL  C13  H132  single  0.970  0.020  1.090
 CRL  C14  SI1   single  1.906  0.020  1.906
 CRL  C14  H141  single  0.970  0.020  1.090
 CRL  C14  H142  single  0.970  0.020  1.090
 CRL  SI1  C15   single  1.883  0.020  1.883
 CRL  SI1  C16   single  1.886  0.020  1.886
 CRL  SI1  C17   single  1.884  0.020  1.884
 CRL  C15  H151  single  0.970  0.020  1.090
 CRL  C15  H152  single  0.970  0.020  1.090
 CRL  C15  H153  single  0.970  0.020  1.090
 CRL  C16  H161  single  0.970  0.020  1.090
 CRL  C16  H162  single  0.970  0.020  1.090
 CRL  C16  H163  single  0.970  0.020  1.090
 CRL  C17  H171  single  0.970  0.020  1.090
 CRL  C17  H172  single  0.970  0.020  1.090
 CRL  C17  H173  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CRL  HN1   N1   C6    115.38  3.000
 CRL  HN1   N1   C1    118.91  3.000
 CRL  C6    N1   C1    117.75  3.000
 CRL  N2    C1   O1    122.57  3.000
 CRL  N2    C1   N1    117.13  3.000
 CRL  O1    C1   N1    120.30  3.000
 CRL  C5    N2   C2    113.01  3.000
 CRL  C5    N2   C1    118.39  3.000
 CRL  C2    N2   C1    124.04  3.000
 CRL  H22   C2   H21   107.25  3.000
 CRL  H22   C2   C3    107.46  3.000
 CRL  H21   C2   C3    110.18  3.000
 CRL  H22   C2   N2    111.86  3.000
 CRL  H21   C2   N2    110.10  3.000
 CRL  C3    C2   N2    109.93  3.000
 CRL  H32   C3   H31   108.14  3.000
 CRL  H32   C3   O2    107.72  3.000
 CRL  H31   C3   O2    110.56  3.000
 CRL  H32   C3   C2    109.44  3.000
 CRL  H31   C3   C2    109.08  3.000
 CRL  O2    C3   C2    111.81  3.000
 CRL  C4    O2   C3    110.59  3.000
 CRL  H42   C4   H41   108.01  3.000
 CRL  H42   C4   C5    109.33  3.000
 CRL  H41   C4   C5    109.62  3.000
 CRL  H42   C4   O2    110.43  3.000
 CRL  H41   C4   O2    107.51  3.000
 CRL  C5    C4   O2    111.85  3.000
 CRL  H52   C5   H51   107.65  3.000
 CRL  H52   C5   C4    110.05  3.000
 CRL  H51   C5   C4    109.05  3.000
 CRL  H52   C5   N2    110.39  3.000
 CRL  H51   C5   N2    109.94  3.000
 CRL  C4    C5   N2    109.72  3.000
 CRL  H6    C6   C14   108.47  3.000
 CRL  H6    C6   C7    108.95  3.000
 CRL  C14   C6   C7    109.38  3.000
 CRL  H6    C6   N1    108.73  3.000
 CRL  C14   C6   N1    110.44  3.000
 CRL  C7    C6   N1    110.82  3.000
 CRL  N3    C7   O3    122.76  3.000
 CRL  N3    C7   C6    114.54  3.000
 CRL  O3    C7   C6    122.58  3.000
 CRL  HN3   N3   C8    117.13  3.000
 CRL  HN3   N3   C7    117.56  3.000
 CRL  C8    N3   C7    123.11  3.000
 CRL  C13   C8   C10   110.96  3.000
 CRL  C13   C8   C9    106.85  3.000
 CRL  C10   C8   C9    108.10  3.000
 CRL  C13   C8   N3    108.58  3.000
 CRL  C10   C8   N3    112.27  3.000
 CRL  C9    C8   N3    109.93  3.000
 CRL  N4    C9   C8    180.00  3.000
 CRL  H102  C10  H101  106.73  3.000
 CRL  H102  C10  C11   108.40  3.000
 CRL  H101  C10  C11   110.23  3.000
 CRL  H102  C10  C8    110.14  3.000
 CRL  H101  C10  C8    108.78  3.000
 CRL  C11   C10  C8    112.41  3.000
 CRL  H112  C11  H111  108.37  3.000
 CRL  H112  C11  S1    106.42  3.000
 CRL  H111  C11  S1    107.36  3.000
 CRL  H112  C11  C10   111.01  3.000
 CRL  H111  C11  C10   112.55  3.000
 CRL  S1    C11  C10   110.88  3.000
 CRL  C12   S1   O5    108.14  3.000
 CRL  C12   S1   O4    109.55  3.000
 CRL  O5    S1   O4    118.60  3.000
 CRL  C12   S1   C11   100.90  3.000
 CRL  O5    S1   C11   108.44  3.000
 CRL  O4    S1   C11   109.75  3.000
 CRL  H122  C12  H121  107.74  3.000
 CRL  H122  C12  C13   113.40  3.000
 CRL  H121  C12  C13   110.47  3.000
 CRL  H122  C12  S1    107.19  3.000
 CRL  H121  C12  S1    106.38  3.000
 CRL  C13   C12  S1    111.34  3.000
 CRL  H132  C13  H131  106.82  3.000
 CRL  H132  C13  C12   109.93  3.000
 CRL  H131  C13  C12   108.24  3.000
 CRL  H132  C13  C8    108.80  3.000
 CRL  H131  C13  C8    109.44  3.000
 CRL  C12   C13  C8    113.40  3.000
 CRL  H142  C14  H141  105.93  3.000
 CRL  H142  C14  SI1   107.05  3.000
 CRL  H141  C14  SI1   109.95  3.000
 CRL  H142  C14  C6    108.51  3.000
 CRL  H141  C14  C6    110.32  3.000
 CRL  SI1   C14  C6    114.66  3.000
 CRL  C17   SI1  C16   108.98  3.000
 CRL  C17   SI1  C15   110.73  3.000
 CRL  C16   SI1  C15   109.90  3.000
 CRL  C17   SI1  C14   107.05  3.000
 CRL  C16   SI1  C14   111.48  3.000
 CRL  C15   SI1  C14   108.66  3.000
 CRL  H153  C15  H152  107.66  3.000
 CRL  H153  C15  H151  107.80  3.000
 CRL  H152  C15  H151  107.52  3.000
 CRL  H153  C15  SI1   111.66  3.000
 CRL  H152  C15  SI1   111.16  3.000
 CRL  H151  C15  SI1   110.86  3.000
 CRL  H163  C16  H162  107.42  3.000
 CRL  H163  C16  H161  107.30  3.000
 CRL  H162  C16  H161  107.90  3.000
 CRL  H163  C16  SI1   110.48  3.000
 CRL  H162  C16  SI1   111.60  3.000
 CRL  H161  C16  SI1   111.93  3.000
 CRL  H173  C17  H172  107.63  3.000
 CRL  H173  C17  H171  107.68  3.000
 CRL  H172  C17  H171  107.52  3.000
 CRL  H173  C17  SI1   111.53  3.000
 CRL  H172  C17  SI1   111.18  3.000
 CRL  H171  C17  SI1   111.12  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CRL  CONST_02  C5    N2   C1   O1     0.00   0.0  0
 CRL  CONST_04  C5    N2   C1   N1   180.00   0.0  0
 CRL  CONST_05  C8    N3   C7   C6   180.00   0.0  0
 CRL  CONST_06  C8    N3   C7   O3     0.00   0.0  0
 CRL  CONST_07  C6    N1   C1   N2   180.00   0.0  0
 CRL  CONST_09  C6    N1   C1   O1     0.00   0.0  0
 CRL  Var_01    O2    C3   C2   N2   -54.98  30.0  1
 CRL  Var_02    O2    C4   C5   N2    55.38  30.0  1
 CRL  Var_03    C4    C5   N2   C2   -52.24  30.0  1
 CRL  Var_04    C5    N2   C2   C3    52.08  30.0  1
 CRL  Var_05    C5    C4   O2   C3   -59.43  30.0  1
 CRL  Var_06    S1    C11  C10  C8   -62.48  30.0  1
 CRL  Var_07    S1    C12  C13  C8    59.60  30.0  1
 CRL  Var_08    C12   S1   C11  C10   54.89  30.0  1
 CRL  Var_09    C13   C12  S1   C11  -53.33  30.0  1
 CRL  Var_10    C15   SI1  C14  C6   -41.37  30.0  3
 CRL  Var_11    H151  C15  SI1  C14   65.95  30.0  3
 CRL  Var_12    H161  C16  SI1  C14  -71.00  30.0  3
 CRL  Var_13    H171  C17  SI1  C14  179.79  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CRL  chir_01  C6  N1  C7   C14  positiv
 CRL  chir_02  C8  C9  C10  C13  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CRL  plan-1  N1   0.020
 CRL  plan-1  C1   0.020
 CRL  plan-1  O1   0.020
 CRL  plan-1  N2   0.020
 CRL  plan-1  C2   0.020
 CRL  plan-1  C5   0.020
 CRL  plan-1  C6   0.020
 CRL  plan-1  HN1  0.020
 CRL  plan-2  C6   0.020
 CRL  plan-2  C7   0.020
 CRL  plan-2  O3   0.020
 CRL  plan-2  N3   0.020
 CRL  plan-2  C8   0.020
 CRL  plan-2  HN3  0.020

